From the moment Coach Jim Harbaugh arrived in San Francisco in 2011, the 49ers have been one of the N.F.L.’s best teams.

In Harbaugh’s first two seasons, the 49ers ranked third in combined wins (24) and points differential (275), trailing only the New England Patriots and the Green Bay Packers in both categories. In those two seasons, San Francisco allowed 502 points, easily the fewest in the league. Even after losing in the Super Bowl in February, Harbaugh’s 49ers seemed poised to become the next dynasty. But after defeating the Packers in Week 1, San Francisco has been outscored, 56-10, in the last two weeks.

In Seattle, the 49ers were 3-point underdogs, and lost, 29-3. At home against the Indianapolis Colts, San Francisco was a 10 ½-point favorite, and lost by 20 points. For the season, San Francisco has fallen short of expectations — defined as the point spread in the game — by an average of 17.5 points a game (only the Giants, at 18.3 points, have been more disappointing). How have teams with similar expectations and results fared over the course of the rest of the season?

From 1990 to 2012, 14 teams have met three criteria: won at least 10 games in the previous year; on average, were favored to win the first three games of the next season; and failed to cover the spread by, on average, at least 10 points. On average, those teams won 12.5 games the previous season but just eight in the season in question, an indication that the slow start is a sign of mediocre things to come.

Team

Year

PF

PA

Spread

Difference

N-1 Record

Year N Rec

NOR

2007

12.7

34.3

-1

-22.7

10-6-0

7-9-0

SFO

2013

14.7

28

-4.2

-17.5

11-4-1

--

DEN

1999

13.7

25.7

-2.3

-14.3

14-2-0

6-10-0

STL

2002

17

25

-5.5

-13.5

14-2-0

7-9-0

NOR

2012

27.7

34

-6.8

-13.2

13-3-0

7-9-0

PIT

2002

15.7

24.3

-4.2

-12.8

13-3-0

10-5-1

NWE

2008

16.3

19.3

-9.2

-12.2

16-0-0

11-5-0

CHI

1992

15.7

26.3

-1.5

-12.2

11-5-0

5-11-0

KAN

2004

20.7

28.7

-3.8

-11.8

13-3-0

7-9-0

TEN

2001

12

23.3

-0.3

-11.7

13-3-0

7-9-0

WAS

2000

17

19.7

-8.8

-11.5

10-6-0

8-8-0

CHI

2007

11

19.3

-3

-11.3

13-3-0

7-9-0

PHI

2003

11

20.3

-1.3

-10.7

12-4-0

12-4-0

ARI

2010

16

25.7

-0.5

-10.2

10-6-0

5-11-0

IND

2008

17.3

22.3

-5

-10

13-3-0

12-4-0

The 2001 St. Louis Rams and the 2006 Chicago Bears lost in the Super Bowl, then both finished 7-9 the next season. The 2006 New Orleans Saints made it to the N.F.C. championship game, then started 2007 with four losses, and finished 7-9. Three games is a small sample size for the 49ers, but last year’s success guarantees nothing but high expectations. And only one of those 14 teams — the 2007 Saints — fell as far short of expectations (as measured by points differential relative to the point spread) as this year’s 49ers.

There might be more hope for a turnaround if San Francisco’s struggles were contained: unfortunately for 49ers fans, the team has struggled in every aspect of the game. The biggest surprise has been the fall of a dominant rush defense.

Two years ago, the 49ers did not allow a rushing touchdown until the 15th game of the season; last year, three of the team’s four linebackers (Aldon Smith, NaVorro Bowman and Patrick Willis) were named first-team All-Pro by The Associated Press, as the run defense finished in the top five in rushing yards, yards per carry and touchdowns allowed.

This season, the 49ers have allowed six rushing touchdowns. The struggles are not just at the goal line: Harbaugh’s 49ers allowed 170 rushing yards just once in his first 38 games (including the postseason). But they have allowed more than that in back-to-back weeks this season against the Seattle Seahawks and the Colts.

Not to nitpick, but how would the comparison group change if you changed being favored in three games to favored in one and a slight dog in a one…?

Chase Stuart

Bob — it’s being an “average” favorite in 3 games, which is what SF was this year. So the 49ers fit in with the control group.

http://www.footballoutsiders.com Danny Tuccitto

Almost all of your points are spot on and pretty indisputable, but I’ll just register my mild disagreement with two of them:

1) “Still, the big names are there on defense, and Tarell Brown, Carlos Rogers and Donte Whitner give the team an above-average secondary. The talented front seven should revert to form, which means the more serious concern might be on offense.”

Carlos Rogers has become a liability in the slot. Tarrell Brown is somehow getting worse with experience. The front seven, as you highlighted, is kind of bereft of talent for the foreseeable future, even with Willis coming back. It’s no coincidence the run D has imploded since their starting NT got hurt. Justin Smith is a shell of his former self. But even more of an indicator to me than all of that is the stat you cited about their last 9 games. They were getting torched…with Culliver…with Willis…with Aldon Smith…with Goldson…and with an NFL-level NT. I just don’t see any evidence that would suggest they’re going to revert to the form of the previous 30 games or so.

2) “Another downgrade was at the other tight end spot, essentially a starting position for the 49ers. With Delanie Walker now with the Tennessee Titans, Vance McDonald and Garrett Celek are playing without much success.”

This one’s just a pet peeve of mine. Not a Walker fan at all. Never have been. He was basically the guy who every color commentator relied on for their “this guy does all the little things” moment of the game, and that’s it. Good special teams player. Above-average blocker, but they already have the best blocking TE in the league. Almost his entire value on offense was his versatility in alignment, which created all kinds of deception for the defense. With Kaepernick, SF wants to go to more of a standard pass-oriented offense than relying on the gimmickery they were forced to use with Smith. Walker flat out had hands of stone, and couldn’t get open on anything other than a wheel route. He would have had even less impact on this offense than he did in the previous one. In the long run, McDonald’s a massive upgrade for what they want to do. He’s a rookie, and pass-catching TEs seem to blossom in Year 2. With Davis out there, McDonald’s growing pains aren’t an issue. When Davis isn’t out there, and he’s forced to carry a bigger load, it’s a disaster.

Chase Stuart

Good stuff, Danny. Don’t really disagree with anything you wrote.

Ty

Is there proof that Justin Smith has fallen off? It is somewhat difficult to quantify the effect of 3-4 DEs, is this based more on game footage?